untested, unfinished

orca_wrap.sh

+#!/bin/bash
+
+# Copyright (c) 2018, Christian Meesters, JGU Mainz 
+# All rights reserved. 
+# 
+# Redistribution and use in source and binary forms, with or without 
+# modification, are permitted provided that the following conditions are met: 
+# 
+#     * Redistributions of source code must retain the above copyright 
+#       notice, this list of conditions and the following disclaimer. 
+#     * Redistributions in binary form must reproduce the above copyright 
+#       notice, this list of conditions and the following disclaimer in the 
+#       documentation and/or other materials provided with the distribution. 
+#     * Neither the name of Christian Meesters or the JGU Mainz nor the names of 
+#       its contributors may be used to endorse or promote products derived 
+#       from this software without specific prior written permission. 
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+# ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE 
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY 
+# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH 
+# DAMAGE.
+
+# ensure clean environment
+module purge
+module load chem/ORCA
+
+# guess a users account
+_arg_assoc=$(sacct -nu "$USER" -o Account%20 | tail -n1 | tr -d '[:space:]')
+
+_arg_queue="parallel"     
+_arg_constraint="broadwell"
+
+SCRIPT="$0"
+SCRIPT_VERSION="0.1"
+
+die()
+{
+        local _ret=$2
+        test -n "$_ret" || _ret=1
+        test "$_PRINT_HELP" = yes && print_help >&2
+        echo "$1" >&2
+        exit ${_ret}
+}
+
+begins_with_short_option()
+{
+        local first_option all_short_options
+        all_short_options='lqscmrh'
+        first_option="${1:0:1}"
+        test "$all_short_options" = "${all_short_options/$first_option/}" && return 1 || return 0
+}
+
+print_help ()
+{
+    echo "This script's help msg"
+    echo 'Usage: ORCA_wrapper [options] <inputdir>'
+    echo
+    printf "\\t%s\\n" "--verbose,--no-verbose: verbose execution (off by default)"
+    printf "\\t%s\\n" "-l,--runlimit: runlimit default is 300 min"
+    printf "\\t%s\\n" "-p,--partition: queue (default is 'parallel')"
+    printf "\\t%s\\n" "-A,--account: account (default is the last submit account; an error is triggered if none specified nor can be deduced)"
+    printf "\\t%s\\n" "--credits: shows credits and version history"
+    printf "\\t%s\\n" "--version: shows the version number"
+    printf "\\t%s\\n" "-h,--help: Prints help"
+
+    echo "Report issues and create feature requests at: https://gitlab.rlp.net/hpc-jgu-physics-simulations/ab-initio-simulations/issues"
+
+    echo "This script will submit itself. DO NOT run it within a job!"
+}
+
+credits()
+{
+   echo "Version is: $SCRIPT_VERSION"
+   echo
+   echo "History of the implementation:"
+   echo "- v0.1   -- 20. Dec. 2018 -- release of the implementation for SLURM, supporting the"
+   echo "                             ability to run multiple ORCA jobs on Mogon II."
+}
+
+# function to redirect simple error messages to stderr
+error() {
+    (>&2 echo -e "ERROR: $1")
+}
+
+warning() {
+    (>&2 echo -e "WARNING: $1")
+}
+
+# command line parsing
+while test $# -gt 0
+do
+        _key="$1"
+        case "$_key" in
+                --test)
+                        _arg_test=on
+                        set -x
+                        ;;
+                --no-verbose|--verbose)
+                        _arg_verbose="on"
+                        test "${1:0:5}" = "--no-" && _arg_verbose="off"
+                        ;;
+                -l*|--runlimit|--runlimit=*)
+                        _val_from_long="${_key##--runlimit=}"
+                        _val_from_short="${_key##-l}"
+                        if test "$_val_from_long" != "$_key"
+                        then
+                                _val="$_val_from_long"
+                        elif test "$_val_from_short" != "$_key" -a -n "$_val_from_short"
+                        then
+                                _val="$_val_from_short"
+                        else
+                                test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+                                _val="$2"
+                                shift
+                        fi
+                        _arg_runlimit="$_val"
+                        ;;
+                -p*|--partition|--partition=*)
+                        _val_from_long="${_key##--partition=}"
+                        _val_from_short="${_key##-p}"
+                        if test "$_val_from_long" != "$_key"
+                        then
+                                _val="$_val_from_long"
+                        elif test "$_val_from_short" != "$_key" -a -n "$_val_from_short"
+                        then
+                                _val="$_val_from_short"
+                        else
+                                test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+                                _val="$2"
+                                shift
+                        fi
+                        _arg_queue="$_val"
+                        ;;
+                -A*|--account|--account=*)
+                        _val_from_long="${_key##--account=}"
+                        _val_from_short="${_key##-A}"
+                        if test "$_val_from_long" != "$_key"
+                        then
+                                _val="$_val_from_long"
+                        elif test "$_val_from_short" != "$_key" -a -n "$_val_from_short"
+                        then
+                                _val="$_val_from_short"
+                        else
+                                test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+                                _val="$2"
+                                shift
+                        fi
+                        _arg_assoc="$_val"
+                        ;;
+                --tag|--tag=*)
+                        _val_from_long="${_key##--tag=}"
+                        _arg_tag=$_val_from_long
+                        ;;
+                -a*|--args|--args=*)
+                        _val_from_long="${_key##--args=}"
+                        _val_from_short="${_key##-a}"
+                        if test "$_val_from_long" != "$_key"
+                        then
+                                _val="$_val_from_long"
+                        elif test "$_val_from_short" != "$_key" -a -n "$_val_from_short"
+                        then
+                                _val="$_val_from_short"
+                        else
+                                test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+                                _val="$2"
+                                shift
+                        fi
+                        _arg_args="$_val"
+                        ;;
+                --dependency|--dependency=*)
+                        _val_from_long="${_key##--dependency=}"
+                        _arg_dependency=$_val_from_long
+                        ;;
+                --constraint|--constraint=*)
+                        _val_from_long="${_key##--constraint=}"
+                        _arg_constraint=$_val_from_long
+                        shift
+                        ;;
+                --credits)
+                        credits
+                        exit 0
+                        ;;
+                --version)
+                        echo "$SCRIPT_VERSION"
+                        exit 0
+                        ;;
+                -h*|--help)
+                        print_help
+                        exit 0
+                        ;;
+                *)
+                        _positionals+=("$1")
+                        ;;
+        esac
+        shift
+done
+
+_positional_names=('_arg_inputdir')
+for (( ii = 0; ii < 2; ii++)); do
+   eval "${_positional_names[ii]}=\${_positionals[ii]}" || die "Error during argument parsing, possibly an Argbash bug." 1
+done
+
+if [ -z "${_arg_assoc}" ]; then
+   error "No account given and, alas, not able to deduce one."
+   print_help
+   exit 1
+fi
+
+if [ -z "${_arg_inputdir}" ]; then
+   error "Found no indicator for the input."
+   print_help
+   exit 1
+fi
+
+### look for samples
+# all possible samples without discrimination:
+samples=$(find -L $(realpath "$_arg_inputdir") -type f \( -iname \*.gjf  \) )
+# transform to array
+
+read -r -a samples <<< $samples
+if [ ${#samples[@]} -eq 0 ]; then
+   error "no input found (was looking for '*gjf' in $_arg_inputdir)."
+   exit 1
+fi
+
+#check if this script is on node by checking env-variable $SLURM_JOB_ID, else send it to SLURM with given parameters and exit 
+if [ -z "$SLURM_JOB_ID" ]; then
+   for sample in "${_arg_inputdir}"/*.gjf; do
+       ### infer job tag
+       if [ -z "$_arg_tag" ]; then
+          _arg_tag="ORCA_$(basename "$_arg_inputdir")_on_$(basename "$sample")_%j"
+       fi
+
+       ### check if output directory already exists
+       if [[ ! -d "${_arg_outdir// }"  ]]; then
+           _arg_outdir="$(pwd)/${_arg_tag}"
+           mkdir -p "${_arg_outdir}"
+       else
+           error "${_arg_outdir// } exists already! Possibly over overwrite of results. Cowardly giving up."
+       fi
+
+       sbatch -A "${_arg_assoc}" -p parallel -J "${_arg_tag}" -o "${_arg_outdir}" -n 40 -t 120:00:00 --signal=B:SIGUSR2@600 -N 1 --wrap "$(cat << EOF
+       cleanup(){
+         cp /localscratch/${SLURM_JOB_ID}/* "\${_arg_outdir}"
+       }
+       trap 'cleanup' SIGUSR2
+       cp $sample /localscratch/\${SLURM_JOB_ID}
+       # Go to jobdir and start the program
+       cd /localscratch/\${SLURM_JOB_ID}
+       set OMPI_MCA_btl=self,sm
+       orca $sample
+       cleanup
+EOF
+)"
+   done
+fi
+
+
+https://stackoverflow.com/questions/53071681/use-of-a-heredoc-with-slurm-sbatch-wrap
+
+
+EOF
+)
+       #./orca.sh ${sample}
+       done
+   fi
+
+
+https://stackoverflow.com/questions/53071681/use-of-a-heredoc-with-slurm-sbatch-wrap
+